ArticleBioinformatics (Oxford, England)2015
AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 65 citations in OpenAlex.
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Epitope mapping strategies for immunogenicity mitigation in streptokinase therapeutics: an in-silico study.Scientific reports · 2025Article
- M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.BMC bioinformatics · 2025Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning.Communications biology · 2023Article
- Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.Nucleic acids research · 2022Article
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.Biophysical reviews · 2022Review
- The structural coverage of the human proteome before and after AlphaFold.PLoS computational biology · 2022Article
- Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance.Journal of the American Chemical Society · 2021Article
- The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization.Protein science : a publication of the Protein Society · 2021Article
- Article
- The Human DNA Mismatch Repair Protein MSH3 Contains Nuclear Localization and Export Signals That Enable Nuclear-Cytosolic Shuttling in Response to Inflammation.Molecular and cellular biology · 2020Article
- SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data.Proteins · 2020Article
- AThe Journal of biological chemistry · 2020Article
- Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.Biophysics and physicobiology · 2020Article
- Revisiting Bap Multidomain Protein: More Than Sticking Bacteria Together.Frontiers in microbiology · 2020Review
- Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal · 2020Review
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
motivationMost proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available.
resultsWe have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with 'inserted' domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. AVAILABILITY AND IMPLEMENTATION: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. CONTACT: adam@sanfordburnham.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.